Algorithms in SNOBOL4 by James F. Gimpel

By James F. Gimpel

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Comp. : Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Ann. Rev. Biophys. Biomol. : Electrostatics calculations: Recent methodological advances and applications to membranes. Curr. Opin. Struct. : Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study. Biophys. : Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation.

Comp. , 18:1848–1862, 1997. [37] C. Sander and R. Schneider. Database of homology-derived protein structures and the structural meaning of sequence alignment. , and Genetics, 9:56–68, 1991. [38] A. Sandu and T. Schlick. Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics. J. Comput. Phys, 151(1):74–113, May 1, 1999. [39] T. Simonson, G. Archontis, and M. Karplus. Free energy simulations come of age: Protein-ligand recognition. Acc.

Figure 3 shows the distance between Pα and O3 in the 1ns simulations of the three model systems. 6Å. 9Å (after 200ps for YC-1 “Flip”–mode simulation and after 800ps for the no–YC-1–mode simulation). These results suggest that different initial binding mode of YC-1 makes a significant difference in terms of YC-1’s effect on GTP catalysis by sGC, and initial “Normal”–mode of binding positively correlates with more chances of cyclization. Dynamics of YC-1 YC-1 does not always stay extended in its binding pocket after initial binding.

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